Chlorinated organic compounds, including tetrachloroethene (PCE) and trichloroethene (TCE), are the most common groundwater contaminants in the United States. These contaminants are also found in soil and sediment at contamination sites. These compounds were commonly used as solvents, dry cleaning agents, and engine degreasers for much of the 20th century and have become some of the most common groundwater contaminants
One method of cleaning up PCE that has become widely used in recent years is bioremediation via reductive dechlorination. In this process, anaerobic microorganisms respire chlorinated solvents, in the process replacing chlorine atoms bound to the carbon with hydrogen atoms. In this way, each chlorine atom on a toxic compound like PCE can be converted to a hydrogen atom in a stepwise process, converting the toxic PCE into relatively harmless ethene.
Some of the organisms most often responsible for carrying out this reductive dechlorination are organohalide-respiring bacterial species, such as species within the genus Dehalococcoides. Dehalococcoides is particularly notable for its ability to dechlorinate certain contaminants that other microorganisms cannot, for example vinyl chloride. However, different strains of Dehalococcoides have been shown to dechlorinate different compounds, as well as being affected by certain environmental parameters to different extents.
An increasing number of environmental consultants offer commercial bioremediation services involving the stimulation of organohalide-degrading bacteria (biostimulation) and/or augmentation of organohalide-degrading bacteria at contaminated sites. However, identification of optimal bioremediation strategies at each site can be challenging, and the efficiency and success of the bioremediation depends on the microbial population at the remediation site and in any microbial cultures used to stimulate or augment the microbial community at the site. Current methods of identification of bacterial strains in mixed microbial communities rely on 16S ribosomal RNA sequencing. Due to high degree of sequence identity between 16S rRNA sequences between strains, it can be difficult to distinguish different strains of organohalide-reducing bacteria within a population.